GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HYR - HYR domain
Pfam: PF02494 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0159
Length: 81
Sequences: 813
Seq/Len: 10.04
HH_delta: 0.569 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
10_C75_C1.029465.905
46_C63_Y0.737924.233
54_F59_T0.426822.448
32_P63_Y0.372062.134
29_W63_Y0.364822.093
11_P77_F0.352432.022
4_T37_N0.311541.787
67_D71_N0.30841.769
63_Y77_F0.2981.709
55_P59_T0.288921.657
2_D6_P0.283551.627
2_D36_D0.281371.614
2_D71_N0.258331.482
60_T76_S0.249431.431
36_D67_D0.243121.395
29_W77_F0.236721.358
50_P63_Y0.235091.349
29_W51_G0.232331.333
6_P36_D0.230621.323
34_A65_A0.224361.287
19_E22_Q0.214831.232
51_G77_F0.210431.207
36_D71_N0.206471.184
24_T53_L0.205661.180
11_P75_C0.205151.177
8_I34_A0.203471.167
51_G54_F0.202731.163
48_H52_D0.202641.162
19_E23_S0.201921.158
66_T72_S0.201271.155
14_I77_F0.197721.134
60_T78_T0.197121.131
62_T74_T0.194371.115
18_V25_A0.192011.101
5_P73_A0.182391.046
9_T78_T0.179451.029
8_I39_G0.178931.026
47_N61_V0.165840.951
47_N51_G0.162570.933
42_V45_T0.160860.923
50_P54_F0.159030.912
3_T59_T0.157180.902
13_D77_F0.155120.890
43_S74_T0.15470.887
74_T80_T0.154310.885
58_T80_T0.150460.863
62_T80_T0.150020.861
22_Q53_L0.148470.852
3_T37_N0.148350.851
27_V32_P0.148050.849
26_S80_T0.147550.846
18_V56_V0.147280.845
16_V25_A0.144910.831
31_E63_Y0.144650.830
14_I79_V0.142760.819
64_T74_T0.141160.810
33_T68_A0.140680.807
12_D61_V0.139750.802
52_D59_T0.13960.801
10_C54_F0.136490.783
33_T81_V0.13570.778
49_P52_D0.134720.773
27_V54_F0.133760.767
18_V81_V0.133640.767
2_D37_N0.132180.758
44_I63_Y0.131620.755
30_T33_T0.131160.752
10_C51_G0.1310.751
34_A37_N0.130090.746
60_T68_A0.128690.738
8_I73_A0.126820.727
48_H77_F0.125610.721
11_P76_S0.125120.718
23_S38_S0.124910.717
7_V43_S0.123510.708
12_D15_T0.123480.708
22_Q62_T0.122180.701
29_W75_C0.121510.697
9_T62_T0.121410.696
53_L64_T0.121160.695
45_T66_T0.121080.695
10_C77_F0.120770.693
11_P14_I0.120410.691
27_V52_D0.11990.688
7_V19_E0.119570.686
60_T81_V0.118250.678
39_G42_V0.117930.676
54_F61_V0.117790.676
34_A39_G0.117590.675
29_W32_P0.117380.673
41_I45_T0.116970.671
12_D17_T0.116870.670
64_T72_S0.115330.662
13_D78_T0.114730.658
28_S32_P0.114410.656
25_A55_P0.114070.654
48_H61_V0.114020.654
25_A80_T0.113970.654
4_T80_T0.113020.648
62_T68_A0.112870.647
7_V35_T0.112640.646
31_E51_G0.112340.644
39_G69_A0.110460.634
62_T76_S0.110340.633
9_T33_T0.110240.632
34_A43_S0.109950.631
16_V30_T0.109850.630
27_V79_V0.109660.629
54_F75_C0.10950.628
30_T35_T0.109070.626
32_P50_P0.109060.626
23_S26_S0.108290.621
54_F77_F0.108150.620
9_T12_D0.107060.614
54_F79_V0.106950.614
42_V65_A0.106460.611
29_W59_T0.106280.610
58_T78_T0.105950.608
11_P51_G0.105770.607
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
2kpnA0.925998.40.569
4hmeA0.913698.10.607
4hmeA0.925997.60.654
3qc5X0.925994.70.759
2yn5A0.950693.90.768
3pddA0.938393.60.772
2yn5A0.938392.50.779
2y3uA0.938391.50.786
1xf1A0.987789.30.796
2yrlA0.938382.60.814
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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